CG-2023-10-17

HL7 Clinical Genomics Weekly Call - Oct 3, 2023 11:00 AM (US Eastern)

HL7 Antitrust Policy

Professional Associations, such as HL7, which bring together competing entities are subject to strict scrutiny under applicable antitrust laws. HL7 recognizes that the antitrust laws were enacted to promote fairness in competition and, as such, supports laws against monopoly and restraints of trade and their enforcement. Each individual participating in HL7 meetings and conferences, regardless of venue, is responsible for knowing the contents of and adhering to the HL7 Antitrust Policy as stated in §05.01 of the Governance and Operations Manual (GOM).

Minutes

Attending the meeting

https://us02web.zoom.us/j/2980068716?pwd=eG9VOXdjTU43VGpJVGNNNGtqbW1qQT09 

Meeting ID: 298 006 8716 // Passcode: 2020

Agenda

Attendees Sign-in

Presiding Co-Chair (Kevin Power - CMH - kmpower@cmh.edu ) 

1.  JD Nolen - CMH - jlnolen@cmh.edu 
2. Soyean Kim CIDGOH SFU ska8@sfu.ca
3. Raja Kathirvel - Philips - raja.kathirvel@philips.com
4. Willie Chang - Epic - willie@epic.com 
5. Bob Dolin - Elimu - bdolin@elimu.io 
6. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
7. Patrick McCormick - IMO - pmccormick@imohealth.com
8. Aly Khalifa - Mayo Clinic - khalifa.aly@mayo.edu 

Agendas and Important Dates 

https://confluence.hl7.org/display/HL7/2024+January+Cycle 

Subgroup reports

• Information Modeling (IM) (Bob F)
• Minutes:
• HL7 CG Information Modeling - Minutes for Oct 2019 to Jan 2020+ 
• Several weeks off .. will bring back more discussion next time
• FHIR (Jamie)
• Minutes:
• FHIR SubGroup Meetings Doc
• tinyurl.com/fhirgenomics 
• Review of biomarker proposal
• OO Work (JD)
• https://jira.hl7.org/browse/FHIR-22147 - Should a reference to device be added as a performer for both Observation and DiagnosticReport 
• More chatter on the above: https://confluence.hl7.org/display/OO/2023-10-16+OO+-+Specimen
• https://jira.hl7.org/browse/FHIR-24863 Ok to reject? 
• IG Maturity (Bret H)
• https://chat.fhir.org/#narrow/stream/179197-genomics/topic/Maturity.20group 
• First meeting held, updating proposed plan. Next step is review within subgroup and finalize. Then there will be a request to present to WG. 

Topic 0: Approval of Minutes from Last Meeting

• https://confluence.hl7.org/display/CGW/CG-2023-10-10 

"You have received the minutes. Are there any corrections to the minutes? (pause) Hearing none, if there are no objections, the minutes are approved"

• Minutes are Approved

Topic 1: Review of pathogen genomics (Soyean)

<presentation from Soyean>

Will have a focus on Data Model in FHIR (with overview of terminology and logic)

Two use cases:

• Clinical
• Patient -> order phenotypic drug susceptibility test -> Obs/Diag Report/Med recommendations
• Might trigger a WGS test in some cases
• Population Health
• Clinical testing might trigger population health monitoring use case -> additional observations/Diag Report/MolSeq (raw and assembly)

Bob D: diff between raw sequence versus assembly?

Soyean: raw is reads, assembly is more refined

Question is more about how resources are related

Bob D: how big will the MolSeq be?

Soyean: 4.5mb

Kevin: 

Usually, DiagRpt points to Observation via .result()

Aly:

Emerging work

Soyean: 

Sounds like work will be based on R4

Topic 2: Discuss Jan 2024 Connectathon

Picture from Bob D:

Operations would be used to read and access VCF data, App could use EHR for clinical data via FHIR queries and GACS for genomic data via Genomic Operations.

Draft of Connectathon 

https://docs.google.com/document/d/1A4Uf5wcIr1OvOc62m3guvMjZZKtPo6tr4a_xILjTwYg/edit#heading=h.sw7c803rr3xf

Willie: GenomeX isn’t focused on the VCF for now

Kevin: Is this an interest for now?

Willie: Yes, but not sure about availability right now.

Bob D: Define the big picture for now and work on smaller pieces in a connectathon. Might get valuable insights.

Kevin: Seems like this is a good ‘big picture’, need to define the smaller slice for connectathon

Bob D: the link above still needs some refinement.

CHAT:

Aly Khalifa to Everyone (Oct 17, 2023, 10:31 AM)

https://build.fhir.org/branches/cg-im-molseq-work_in_progress_2/observation.html

Obs.valueReference

https://build.fhir.org/branches/cg-im-molseq-work_in_progress_2/molecularsequence.html

work in progress

+1

https://hl7.org/fhir/R4/molecularsequence.html

R4: Obs.derivedFrom

Bob Dolin to Everyone (Oct 17, 2023, 10:36 AM)

http://hl7.org/fhir/uv/genomics-reporting/histocompatibility.html

Helpful info

Vote template

Vote: <describe the motion here>

Mover/Seconder: <makes the motion/second:: Name1/Name 2>

Discussion: <ask for and document discussions>

For-Against-Abstain – <document vote: X-Y-Z>

Motion <passes/fails>

chat.fhir.org (zulip) comments

• Genomics
• If you would like to bring up a topic for discussion, Zulip is the platform and the stream is genomics - https://chat.fhir.org/#narrow/stream/179197-genomics 

Future proposed agenda topics/requests 

• WG members: please use this section to request topics to cover on our WG calls

https://confluence.hl7.org/display/CGW/Future+Topics+for+Weekly+Meetings Needs review/clean up

Jira for change requests

• If you like to open a ticket, Jira is the platform - https://jira.hl7.org/secure/Dashboard.jspa?selectPageId=12002 

External efforts (updates welcome)

• GenomeX/CodeX Accelerator (hosted through CodeX) (Arthur Hermann)
• Arthur to provide updates as needed https://confluence.hl7.org/display/COD/Genomics 
• GA4GH (Global Alliance for Genomics and Health)
• Genomic Knowledge Standards (GKS) Work Stream (leads: Bob Freimuth, Andy Yates)
• Variant Representation subgroup (lead by Larry Babb/Alex Wagner)
• See ongoing project board at https://github.com/orgs/ga4gh/projects/5
• VRS 1.3 (structural variation) anticipated by Dec 2021
• Variant Annotation subgroup (lead by Matt Brush and Javi Lopez)
• Working on statements about therapeutic interventions and variant pathogenicity
• https://docs.google.com/spreadsheets/d/1zQU-Yv7gB7IHKIOVsTh-74BwdtgB9KQpKcWkSHZOa-Q/edit
• V0 release: 4 core substatement types + generalized model
• Due "soon"
• Sequence Annotation subgroup (lead by Karen Eilbeck and Shawn Rynearson)
• Clinical & Phenotypic Data Capture Work Stream
• Pedigree Activity (Grant Wood)
• help GA4GH community to understand HL7 Pedigree standards
• https://docs.google.com/spreadsheets/d/1AxRufaSICADO_f9CAhbkVh5dChT4FjHZgvGFFdC-2WI/edit
• Phenopackets
• Under continuous development
• Currently going through the ISO
• G2MC (Grant Wood)
• Looking to develop AI tool for literature review for poly-genetic risk, generate guidance
• Create KB on G2MC website 
• ClinGen/ClinVar (Larry Babb)
• Data Exchange/Platform WG, major driver project of GA4GH GKS
• will discuss further when Larry in on a call
• ONC Sync for Genes (Bob Freimuth)
• ONC website: https://www.healthit.gov/topic/sync-genes
• Phase 5 briefing from Bob Dolin here.
• ISO TC/215 Genomics Subcommittee (Liz, Clem, Bob F)
• Canada is sponsoring a phenopackets spec in ISO, will be based on the GA4GH spec that was approved fall 2019
• The technical experts group just convened to work on this (mid Aug)
• Since Phenopackets is implementing the GA4GH VR spec, which we are attempting to keep aligned with the CG IM, this work will be of interest to the CG WG
• Arthur to review for other standards that might overlap with CG
• Bob M / Bob F: Liaison through HL7
• Cannot share documents, but we can talk about them
• mCODE (May Terry)
• mCODE STU3 passed ballot approval. Currently in reconciliation with publication ETA in Sept 2023.

WG projects and outreach